Longtail tuna, an important pelagic species, little known about the biological studies widely distributes in tropical to temperate waters of the Indo-Pacific Ocean. In this study, the mitochondrial D-loop sequences were used in population genetic structure studies in the longtail tuna from eastern Taiwan waters. Total of 195 samples by set-net and longline of the longtail tuna were collected for DNA samples from December 2005 to March 2012, on the eastern coast of Taiwan. The results showed that the longtail tuna in the waters of east Taiwan as a single ethnic group, highly individual polymorphic, and with no significant population differentiation within the sample.